Dear Lammps Users,
Please help if you have some experience with the fix deform commands. Generally speaking, The structure is not deforming correspond to the simulation box. I used keyword “remap x”. So my question is with this fix deform command, It there anything that I need to beware of? Do I need to use a tight cube box? If you are interested, please email me back and I will send you the .lammpstrj dump file which you could check in VMD to understand what I am saying. They are less then 20MB.
For detailed information, please read the following:
I followed this tutorial which is about amorphous Polyethylene deformation:
https://icme.hpc.msstate.edu/mediawiki/index.php/Deformation_of_Amorphous_Polyethylene
here is the input script website:https://icme.hpc.msstate.edu/mediawiki/index.php/LAMMPS_Input_Deck_for_Atomistic_Deformation_of_Amorphous_Polyethylene
Basically, it is first doing 4 stages of equilibration with NVE, NPT, NPT and NPT. secondly fix NPT at a specific temperature and deform the simulation box in x direction, then measure the pressure on the boundary and generate the stress-strain curve.
By changing the running steps in each Equilibration stage to ten times larger (e.g. 10000 => 100000 running steps). By also using their input data file (it is 1000 atoms/chain *10 chain, totally 10000 atoms ) I successfully repeated the researcher’s result.
Now I generated a polyethylene structure data file (also 10000 atoms with 10 chain) with Avogadro and VMD, then run in Lammps with the exactly same input script, but sometimes when I checked the result, I found the PE structure only deformed a little bit, the deformation is not correspond to the simulation box.
I have tried changing the initial box as a cube or a rectangle before doing the equilibration. Which the cube box is kind of loose, you have 10 A between the box boundary and the nearest inner atoms in x direction and tight in y,z direction. The rectangle simulation is a tight fit of the atom structure. which each direction has maximum 1-2 A, and the length of box on y and z direction are equal.
The result is, for the cube box, I got only like 0.03 strain. For the rectangle box, I can got 0.2 strain, then the box deform but the PE structure did not move very much. then I tried both case with deformation in the Y axis and in all cases they deformed very well.
Thanks to all of you.
Yueqi Hu